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At least 559 records · Page 31

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kinetic closures for unmagnetized and magnetized plasmas

Parallel and perpendicular closures with cyclotron resonance effects retained for the five-moment (density, temperature, and flow velocity) fluid equations are derived by solving the kinetic equation with the Bhatnagar–Gross–Krook operator in Fourier space. For parallel propagation, the parallel closures are reduced to those of Ji et al. [Phys. Plasmas 20, 082121 (2013)]. The closures when combined to the fluid equations reproduce the fully kinetic dispersion relation that can be directly derived from the kinetic equation. The closures for the five-moment fluid system can be utilized to derive closures for the extended fluid system, which is demonstrated by deriving closures for the ten-moment system consisting of density, flow velocity, temperature, and viscosity tensor equations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

First characterisation of the MAGO cavity, a superconducting RF detector for kHz–MHz gravitational waves

Heterodyne detection using microwave cavities is a promising method for detecting high-frequency gravitational waves (GWs) or ultralight axion dark matter. In this work, we report on studies conducted on a spherical 2-cell cavity developed by the MAGO collaboration for high-frequency GWs detection. Although fabricated around 20 years ago, the cavity had not been used since. Due to deviations from the nominal geometry, we conducted a mechanical survey and performed room-temperature plastic tuning. Measurements and simulations of the mechanical resonances and electromagnetic properties were carried out, as these are critical for estimating the cavity’s GW coupling potential. Based on these results, we plan further studies in a cryogenic environment. The cavity characterisation does not only provide valuable experience for a planned physics run but also informs the future development of improved cavity designs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Gyrokinetic simulations of the effects of magnetic islands on microturbulence in KSTAR

Gyrokinetic simulations are utilized to study effects of magnetic islands (MIs) on the ion temperature gradient (ITG) turbulence in the KSTAR tokamak with resonant magnetic perturbations. Simulations show that the transport is controlled by the nonlinear interactions between the ITG turbulence and self-generated vortex flows and zonal flows, leading to an anisotropic structure of fluctuation and transport on the poloidal plane and in the toroidal direction. MIs greatly enhance turbulent transport of both particle and heat. The turbulent transport exhibits variations in the toroidal direction, with transport through the resonant layer near the island X-point being enhanced when the X-point is located at the outer mid-plane. A quantitative agreement is shown between simulations and KSTAR experiments in terms of time frequency and perpendicular wavevector spectrum.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sub-Doppler Cooling of a Trapped Ion in a Phase-Stable Polarization Gradient

Trapped ions provide a highly controlled platform for quantum sensors, clocks, simulators, and computers, all of which depend on cooling ions close to their motional ground state. Existing methods like Doppler, resolved sideband, and dark resonance cooling balance trade-offs between the final temperature and cooling rate. A traveling polarization gradient has been shown to cool multiple modes quickly and in parallel, but utilizing a stable polarization gradient can achieve lower ion energies, while also allowing tailorable light-matter interactions in the sub-wavelength regime. In this Letter, we demonstrate cooling of a trapped ion below the Doppler limit using a phase-stable polarization gradient created using trap-integrated photonic devices. At an axial frequency of 2⁢𝜋×1.45 MHz we achieve ⟨𝑛⟩=1.56±0.07 in 150 μ⁢s and cooling rates of ∼0.3 quanta/μ⁢s. Here, we examine ion dynamics under different polarization gradient phases, detunings, and intensities, showing reasonable agreement between experimental results and a multilevel model. Cooling is fast and power efficient, with lower average motional Fock state occupation when compared to simulated operation under the corresponding running wave configuration. Our results demonstrate a well-controlled test bed for studying the dynamics of multilevel atomic systems in a phase-stable polarization gradient.

Atom & ion cooling↗

Uniaxial stress study of spin and charge stripes in La1.875Ba0.125CuO4 by 139La NMR and 63Cu NQR

We study the response of spin and charge order in single crystals of La1.875Ba0.125CuO4 to uniaxial stress, through 139La nuclear magnetic resonance (NMR) and 63Cu nuclear quadrupole resonance (NQR), respectively. In unstressed La1.875Ba0.125CuO4, the low-temperature tetragonal structure onsets below TLTT = 57 K, while the charge order and the spin order transition temperatures are TCO = 54 K and TSO = 37 K, respectively. We find that uniaxial stress along the [110] lattice direction strongly suppresses TCO and TSO, but has little effect on TLTT. In other words, under stress along [110] a large splitting (≈ 21 K) opens between TCO and TLTT, showing that these transitions are not tightly linked. On the other hand, stress along [100] causes a slight suppression of TLTT but has essentially no effect on TCO and TSO. Magnetic field H along [110] stabilizes the spin order: the suppression of TSO under stress along [110] is slower under H ∥ [110] than H ∥ [001]. We develop a Landau free energy model and interpret our findings as an interplay of symmetry breaking terms driven by the orientation of spins.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Cross Section Generation Capability in Griffin

The Griffin code is a Multiphysics Object-Oriented Simulation Environment (MOOSE) based reactor multiphysics analysis application jointly developed by Idaho National Laboratory and Argonne National Laboratory. The code includes a variety of steady-state solvers for fixed-source, k-eigenvalue, adjoint, and subcritical multiplication, as well as transient solvers for point-kinetics, improved quasi-static, and spatial dynamics. The code reads multigroup cross sections in the ISOXML format generated from external deterministic or Monte Carlo cross section generation codes. The implementation of the cross section generation capability in Griffin was initiated last year by plugging in the cross section application programming interface (CSAPI) and reviewing the methodologies for treating particulate fuels. The focus this year was on improving the CSAPI integration and implementing advanced self-shielding methods for applications to advanced reactor problems with TRISO fuels. First, the process for cross section library generation was updated to accurately and rigorously produce isotopic cross section data. Second, the equivalent Dancoff factor cell method performing slowing down calculations on the fly for the resonance treatment was implemented in CSAPI to improve the accuracy of effective multigroup cross sections in the resonance energy range. Third, the iterative local spatial self-shielding method was implemented under the calculation framework of the equivalent Dancoff factor cell method to accurately deal with the double heterogeneity effect of particulate fuel. The updated CSAPI with the advanced self-shielding methods, together with the cross section libraries generated based on the improved process, were tested for pin-cell, unit-cell, and fuel assembly problems with various resonance self-shielding conditions based on very high temperature reactor, high temperature test reactor, and Empire benchmark cores, indicating that the updated CSAPI in Griffin is able to produce multigroup cross sections accurately and efficiently. We also showed that the methodology worked well for pebble bed fuel from HTR-10, but the capability still needs to be fully integrated into CSAPI. In the future, further benchmark tests will be performed for various thermal reactor core problems, including particulate fuel-based pebble bed reactors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Synthesis of nanodiamonds encapsulated by zeolitic imidazole framework-8 for quantum sensing applications

Nitrogen vacancy (NV)-containing nanodiamonds are widely used in quantum sensing applications due to their high sensitivity to magnetic fields, relatively low cost, and ability to be initialized, manipulated, and read out at room temperature. Quantum sensing techniques such as optically detected magnetic resonance (ODMR) and spin relaxometry have exploited the sensitivity of the NV nanodiamonds to magnetic fields to detect a range of analytes, such as pH, metal ions, and biomolecules. However, diversifying the sensing targets accessible by NV diamond quantum sensors typically requires careful engineering of the diamond surface chemistry with stimuli-responsive functional groups. Here, a simple protocol for coating NV nanodiamonds with the zeolitic imidazole framework 8 (ZIF-8), a widely used metal-organic framework, is presented. ZIF-8 is a highly porous material that has been used as a selective sensor for gasses, metal ions, and other analytes. The material is well-characterized by x-ray diffraction, transmission electron microscopy, scanning electron microscopy, x-ray photoelectron spectroscopy, and luminescence spectroscopy. Encapsulation of NV nanodiamonds with a porous scaffold such as ZIF-8 provides a promising method for improving the selectivity for the quantum sensing of various analytes. Importantly, the ZIF-8 coating does not impact the luminescence properties of the NV diamond, which is a key readout in ODMR and spin relaxometry sensing approaches. Indeed, the ODMR spectra with and without the ZIF-8 shell is nearly identical. Moreover, the ZIF-8 coating increases the longitudinal spin relaxation time of the NV nanodiamond by a factor of 4 relative to aggregated diamond, a desirable outcome for spin relaxation-based quantum sensing. Metal-organic framework composites with nanodiamonds thus are an exciting strategy for enhancing NV nanodiamond performance in applications such as quantum sensing and quantum-enhanced nuclear magnetic resonance spectroscopy.

nitrogen vacancy nanodiamond↗

Experimental Investigation of Plasma Processing for PIP-II SSR2 Cavities

Field emission and multipacting are critical factors that limit the achievable operational gradient of superconducting radio frequency (SRF) cavities. Plasma processing (PP) has been demonstrated as an effective in-situ technique for mitigating hydrocarbon-induced field emission and multipacting across a range of cavity geometries. In this work, we present the initial development and subsequent application of plasma processing for PIP-II type II spoke resonators (SSR2). The process was carried out at room temperature on an SSR2 cavity equipped with the CM-style high-power coupler and installed in the cryostat. Cavity performance was evaluated through comparative cold tests conducted before and after plasma processing.

Giaccone, Bianca [Fermilab] (ORCID:000000027275846↗

High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes

Photosystem I (PSI) is one of the two main pigment–protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI 3 ), PSI 3 mutants, and PSI 3 –IsiA 18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure–function relationship. We will focus on the so-called “red antenna states” of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI 3 and PSI 3 -IsiA 18 supercomplexes allowed us to make inferences about EET from the IsiA 18 ring to the PSI 3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA 18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA 18 ring to the PSI 3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Acoustic chamber for weightless positioning

The objective of this work is to perfect and extend the acoustic position technique that was developed at JPL for use in the future Space Processing Laboratory in Space. The main effort is centered on design of a position device for processing of molten materials. Namely, a resonator has the capability of positioning in an extreme temperature gradient and a frequency servo loop to maintain it there as the temperature varies.

Wang, T. G.↗

Ferromagnetic resonance studies of thermal effects on lunar metallic Fe phases

Ferromagnetic resonance results of annealing experiments are discussed which illustrate the thermal effects on lunar metallic iron phases already present in a lunar fines sample. Spectral features of ferromagnetic resonance produced in the sample by heat treatments at temperatures between 600 and 1025 C are described which resemble those detected in lunar breccias and crystalline rocks. A correlation is shown to exist between these features and the degree of thermal metamorphism. It is noted that this correlation can be used as a built-in geothermometer or probe to investigate the thermal history and degree of metamorphism of a lunar sample containing metallic iron phases. The thermal history of a metaclastic rock is analyzed in this way, and it is shown that thermal metamorphism is an effective process for increasing relaxation times or the stability of the natural remanent magnetization carried by single-domain metallic iron particles.

Tsay, F.-D.↗

Kinetics of the reaction OH + D yields OD + H

The reaction of OH radicals with D-atoms to form OD has been studied at room temperature in a discharge-flow system utilizing UV resonance fluorescence detection of the molecular species. A rate constant of approximately 1.3 by 10 to the -10th power cu cm per sec is reported where the error limits include systematic error estimates. Astrophysical and kinetic implications are discussed briefly.

Margitan, J. J.↗

Supersonic-nitrogen flow-field measurements with the resonant Doppler velocimeter

The application of the resonant Doppler velocimeter (RDV) for obtaining the mean velocity, temperature, and pressure measurements and flow-field visualization in a supersonic free nitrogen jet is reported. This method utilizes laser-induced fluorescence to determine the spectral absorption of an atomic or molecular species seeded into the flow. A narrow linewidth tunable laser is directed into the flow and the total fluorescence from any point is obtained as the laser is tuned. The velocity of the flow is obtained from the Doppler shifted absorption frequency, and the temperature and pressure of the gas are determined from line broadening measurements. Results are presented for the use of this technique to determine the velocity, temperature, and pressure of the flow of sodium atoms seeded into a supersonic nitrogen jet. It is concluded that the visible signal is sufficiently intense for spatially resolved flow visualization purposes.

Cheng, S.↗

Chromospheric activity and TiO bands in M giants

Low-resolution IUE spectra of 23 cool giant stars ranging from K3 through M6 have been used to examine chromospheric activity in late-type giants. Previous studies have suggested a decrease in the fractional flux, normalized to bolometric flux, of the Mg II resonance lines (an indicator of chromospheric activity) with effective temperature. Using more accurately determined effective temperatures, this decrease is confirmed and found to be more rapid than previously suggested. A strong correlation is found between relative TiO band strengths, as measured by the Wing TiO index, and the level of chromospheric activity, as measured by Mg II fluxes. Cool giants which have weak TiO bands relative to the mean TiO strengths for stars of similar color also have Mg II lines that are weaker than the mean. Changes in composition and in chromospheric activity as a consequence of aging are suggested as a possible origin of this interesting relation.

Steiman-Cameron, T. Y.↗

Detailed mechanism of toluene oxidation and comparison with benzene

A detailed mechanism for the oxidation of toluene in both argon and nitrogen dilutents is presented. The mechanism was used to compute experimentally ignition delay times for shock-heated toluene-oxygen-argon mixtures with resonably good success over a wide range of initial temperatures and pressures. Attempts to compute experimentally measured concentration profiles for toluene oxidation in a turbulent reactor were partially successful. An extensive sensitivity analysis was performed to determine the reactions which control the ignition process and the rates of formation and destruction of various species. The most important step was found to be the reaction of toluene with molecular oxygen, followed by the reactions of hydroperoxyl and atomic oxygen with benzyl radicals. These findings contrast with the benzene oxidation, where the benzene-molecular oxygen reaction is quite unimportant and the reaction of phenyl with molecular oxygen dominates. In the toluene mechanism the corresponding reaction of benzyl radicals with oxygen is unimportant. Two reactions which are important in the oxidation of benzene also influence the oxidation of toluene for several conditions. These are the oxidations of phenyl and cyclopentadienyl radicals by molecular oxygen. The mechanism presented successfully computes the decrease of toluene concentration with time in the nitrogen diluted turbulent reactor. This fact, in addition to the good prediction of ignition delay times, shows that this mechanism can be used for modeling the ignition and combustion process in practical, well-mixed combustion systems.

Bittker, David A.↗